A twelve-treatment experiment with the main plot (three water treatments:30% increase (W), 30% reduction (R), and natural rainfall (CK) and split-plot (4 nitrogen gradients:0 (N0), 30 (N30), 50 (N50) and 100 (N100) kg/(hm²·a) was designed in Stipa breviflora desert steppe to investigate the diversity and composition of arbuscular mycorrhizal fungi (AMF) community in soil by high-throughput sequencing. The results showed that increased moisture content promoted but nitrogen addition inhibited alpha diversity of AMF. The interaction between water increase and nitrogen addition promoted alpha diversity of AMF and changed the composition of AMF communities. Water increase increased aboveground biomass of various plants, nitrogen addition significantly increased the biomass of perennial weeds, semi-shrub and undershrub, but significantly reduced the biomass of perennial grasses. In addition, the relative abundance of Diversisporaceae was significantly and positively correlated with the biomass of biennial plants, semi-shrub and undershrub. The biomass of biennial plants, semi-shrub and undershrub increased with nitrogen addition and rainfall enhancement. This study demonstrates the stability of AMF community structure under short-term climate change. In addition, the correlation between the abundance of AMF and the biomass of various life forms of vegetation proves that AMF have strong connectivity with vegetation in ecosystems with relatively scarce nutrient resources.